>> In general, seqid + seqheader seems the most useful
>> combination in terms of fasta http://en.wikipedia.org/wiki/FASTA_format
>> assuming that the full line is a header (id + desc).
I also vote in favour of seqid + seqheader.
> Also, I think one should be able to work with sequences as far as
> possible without resorting to Bytestring operations (exposing the
> internals).
> Is it okay to use Monoid for appending and (m)empty? And have separate
> 'slice' and 'copy' (or perhaps 'defragment')?
>
This sounds interesting to me, but the stuff about Monoid is over my head.
What would be the purpose of the 'slice' and 'copy' functions?
Dan Fornika
dforn...@gmail.com
On 2012-12-10, at 3:54 AM, Ketil Malde wrote:
> Christian Höner zu Siederdissen <choe...@tbi.univie.ac.at> writes:
>
>> do you want to have certain laws? Like header = id + (" " +)
>> description? In general, seqid + seqheader seems the most useful
>> combination in terms of fasta http://en.wikipedia.org/wiki/FASTA_format
>> assuming that the full line is a header (id + desc). Of course, that
>> would be a "3." -- and I am ignoring all other formats out there that
>> could be BioSeq's.
>
> Yes, it strikes me as perhaps the best option: add seqid and seqheader,
> remove seqlabel from the class, but make it a separate alias with a
> deprecation warning.
>
> Anyone opposed?
>
> Also, I think one should be able to work with sequences as far as
> possible without resorting to Bytestring operations (exposing the
> internals).
>
> Is it okay to use Monoid for appending and (m)empty? And have separate
> 'slice' and 'copy' (or perhaps 'defragment')? Any implementor of the
> classes would have to bear the burden of implementing this as well, of
> course.
>
> -k
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